Please wait a minute...
Protein & Cell

ISSN 1674-800X

ISSN 1674-8018(Online)

CN 11-5886/Q

邮发代号 80-984

2019 Impact Factor: 10.164

Protein & Cell  2024, Vol. 15 Issue (7): 475-492   https://doi.org/10.1093/procel/pwad057
  本期目录
Long way up: rethink diseases in light of phase separation and phase transition
Mingrui Ding1,2,3, Weifan Xu1,2,3, Gaofeng Pei1,2, Pilong Li1,2()
1. State Key Laboratory of Membrane Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
2. Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
3. NuPhase Therapeutics, Beijing 100083, China
 全文: PDF(11857 KB)  
Abstract

Biomolecular condensation, driven by multivalency, serves as a fundamental mechanism within cells, facilitating the formation of distinct compartments, including membraneless organelles that play essential roles in various cellular processes. Perturbations in the delicate equilibrium of condensation, whether resulting in gain or loss of phase separation, have robustly been associated with cellular dysfunction and physiological disorders. As ongoing research endeavors wholeheartedly embrace this newly acknowledged principle, a transformative shift is occurring in our comprehension of disease. Consequently, significant strides have been made in unraveling the profound relevance and potential causal connections between abnormal phase separation and various diseases. This comprehensive review presents compelling recent evidence that highlight the intricate associations between aberrant phase separation and neurodegenerative diseases, cancers, and infectious diseases. Additionally, we provide a succinct summary of current efforts and propose innovative solutions for the development of potential therapeutics to combat the pathological consequences attributed to aberrant phase separation.

Key wordsmultivalency    compartments    aberrant phase separation    therapeutics    gain or loss of phase separation    diseases
收稿日期: 2023-10-12      出版日期: 2024-07-31
Corresponding Author(s): Pilong Li   
 引用本文:   
. [J]. Protein & Cell, 2024, 15(7): 475-492.
Mingrui Ding, Weifan Xu, Gaofeng Pei, Pilong Li. Long way up: rethink diseases in light of phase separation and phase transition. Protein Cell, 2024, 15(7): 475-492.
 链接本文:  
https://academic.hep.com.cn/pac/CN/10.1093/procel/pwad057
https://academic.hep.com.cn/pac/CN/Y2024/V15/I7/475
1 EW Abd El-Wahab, RP Smyth, E Mailler et al. Specific recognition of the HIV-1 genomic RNA by the Gag precursor. Nat Commun 2014;5:4304.
https://doi.org/10.1038/ncommS5304
2 YA Abramzon, P Fratta, BJ Traynor et al. The overlapping genetics of amyotrophic lateral sclerosis and frontotemporal dementia. Front Neurosci 2020;14:42.
https://doi.org/10.3389/fnins.2020.00042
3 A Aguzzi, M Altmeyer. Phase separation: linking cellular compartmentalization to disease. Trends Cell Biol 2016;26:547–58.
https://doi.org/10.1016/j.tcb.2016.03.004
4 RM Ahmed, M Irish, O Piguet et al. Amyotrophic lateral sclerosis and frontotemporal dementia: distinct and overlapping changes in eating behaviour and metabolism. Lancet Neurol 2016;15:332–42.
https://doi.org/10.1016/S1474-4422(15)00380-4
5 F Aktar, C Burudpakdee, M Polanco et al. The huntingtin inclusion is a dynamic phase-separated compartment. Life Sci Alliance 2019;2:e201900489.
https://doi.org/10.26508/lsa.201900489
6 NH Alami, RB Smith, MA Carrasco et al. Axonal transport of TDP-43 mRNA granules is impaired by ALS-causing mutations. Neuron 2014;81:536–43.
https://doi.org/10.1016/j.neuron.2013.12.018
7 S Alberti, D Dormann. Liquid-liquid phase separation in disease. Annu Rev Genet 2019;53:171–94.
https://doi.org/10.1146/annurev-genet-112618-043527
8 M Alenquer, S Vale-Costa, TA Etibor et al. Influenza A virus ribonucleoproteins form liquid organelles at endoplasmic reticulum exit sites. Nat Commun 2019;10:1629.
https://doi.org/10.1038/S41467-019-09549-4
9 M Alriquet, G Calloni, A Martinez-Limon et al. The protective role of m1A during stress-induced granulation. J Mol Cell Biol 2021;12:870–80.
https://doi.org/10.1093/jmcb/mjaa023
10 S Ambadipudi, J Biernat, D Riedel et al. Liquid-liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau. Nat Commun 2017;8:275.
https://doi.org/10.1038/S41467-017-00480-0
11 PEA Ash, S Lei, J Shattuck et al. TIa1 potentiates tau phase separation and promotes generation of toxic oligomeric tau. Proc Natl Acad Sci U S A 2021;118:e2014188118.
https://doi.org/10.1073/pnas.2014188118
12 CA Azaldegui, AG Vecchiarelli, JS Biteen. The emergence of phase separation as an organizing principle in bacteria. Biophys J 2020;120:1123–38.
https://doi.org/10.1016/j.bpj.2020.09.023
13 WM Babinchak, BK Dumm, S Venus et al. Small molecules as potent biphasic modulators of protein liquid-liquid phase separation. Nat Commun 2020;11:5574.
https://doi.org/10.1038/S41467-020-19211-z
14 SF Banani, AM Rice, WB Peeples et al. Compositional control of phase-separated cellular bodies. Cell 2016;166:651–63.
https://doi.org/10.1016/j.cell.2016.06.010
15 SF Banani, HO Lee, AA Hyman et al. Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol 2017;18:285–98.
https://doi.org/10.1038/nrm.2017.7
16 S Bernacchi, EW Abd El-Wahab, N Dubois et al. HIV-1 Pr55Gag binds genomic and spliced RNAs with different affinity and stoichiometry. RNA Biol 2017;14:90–103.
https://doi.org/10.1080/15476286.2016.1256533
17 S Boeynaems, S Alberti, NL Fawzi et al. Protein phase separation: a new phase in cell biology. Trends Cell Biol 2018;28:420–35.
https://doi.org/10.1016/j.tcb.2018.02.004
18 JJ Bouchard, JH Otero, DC Scott et al. Cancer mutations of the tumor suppressor SPOP disrupt the formation of active, phase-separated compartments. Mol Cell 2018;72:19–36.e8.
https://doi.org/10.1016/j.molcel.2018.08.027
19 S Boyko, X Qi, TH Chen et al. Liquid-liquid phase separation of tau protein: the crucial role of electrostatic interactions. J Biol Chem 2019;294:11054–9.
https://doi.org/10.1074/jbc.AC119.009198
20 S Brocca, R Grandori, S Longhi et al. Liquid-liquid phase separation by intrinsically disordered protein regions of viruses: roles in viral life cycle and control of virus-host interactions. Int J Mol Sci 2020;21:9045.
https://doi.org/10.3390/ijmS21239045
21 P Chadha, J Han, JL Starkey et al. Regulated interaction of tegument proteins UL16 and UL11 from herpes simplex virus. J Virol 2012;86:11886–98.
https://doi.org/10.1128/JVI.01879-12
22 B Chong, M Li, T Li et al. Conservation of potentially druggable cavities in intrinsically disordered proteins. ACS Omega 2018;3:15643–52.
https://doi.org/10.1021/acsomega.8b02092
23 V Cohen-Kaplan, I Livneh, A Ciechanover. Proteasome phase separation: a novel layer of quality control. Cell Res 2020;30:374–5.
https://doi.org/10.1038/S41422-020-0306-9
24 J Cubuk, JJ Alston, JJ Incicco et al. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nat Commun 2021;12:1936.
https://doi.org/10.1038/S41467-021-21953-3
25 M Dang, J Song. ALS-causing D169G mutation disrupts the ATP-binding capacity of TDP-43 RRM1 domain. Biochem Biophys Res Commun 2020;524:459–64.
https://doi.org/10.1016/j.bbrc.2020.01.122
26 A Danieli, S Martens. p62-mediated phase separation at the intersection of the ubiquitin-proteasome system and autophagy. J Cell Sci 2018;131:jcS214304.
https://doi.org/10.1242/jcs.214304
27 O Delattre, J Zucman, B Plougastel et al. Gene fusion with an ETS DNA-binding domain caused by chromosome translocation in human tumours. Nature 1992;359:162–5.
https://doi.org/10.1038/359162a0
28 M DiFiglia, E Sapp, KO Chase et al. Aggregation of huntingtin in neuronal intranuclear inclusions and dystrophic neurites in brain. Science 1997;277:1990–3.
https://doi.org/10.1126/science.277.5334.1990
29 M Du, ZJ Chen. DNA-induced liquid phase condensation of cGAS activates innate immune signaling. Science 2018;361:704–9.
https://doi.org/10.1126/science.aat1022
30 T Dubnikov, T Ben-Gedalya, E Cohen. Protein quality control in health and disease. Cold Spring Harb Perspect Biol 2017;9:a023523.
https://doi.org/10.1101/cshperspect.a023523
31 R Düster, IH Kaltheuner, M Schmitz et al. 1, 6-Hexanediol, commonly used to dissolve liquid-liquid phase separated condensates, directly impairs kinase and phosphatase activities. J Biol Chem 2021;296:100260.
https://doi.org/10.1016/j.jbc.2021.100260
32 JR Espinosa, JA Joseph, I Sanchez-Burgos et al. Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components. Proc Natl Acad Sci USA 2020;117:13238–47.
https://doi.org/10.1073/pnas.1917569117
33 M Feric, N Vaidya, TS Harmon et al. Coexisting liquid phases underlie nucleolar subcompartments. Cell 2016;165:1686–97.
https://doi.org/10.1016/j.cell.2016.04.047
34 R Ferrari, D Kapogiannis, ED Huey et al. FTD and ALS: a tale of two diseases. Curr Alzheimer Res 2011;8:273–94.
https://doi.org/10.2174/156720511795563700
35 RA Fisher, B Gollan, S Helaine. Persistent bacterial infections and persister cells. Nat Rev Microbiol 2017;15:453–64.
https://doi.org/10.1038/nrmicro.2017.42
36 MK Floeter, TF Gendron. Biomarkers for amyotrophic lateral sclerosis and frontotemporal dementia associated with hexanucleotide expansion mutations in C9orF72. Front Neurol 2018;9:1063.
https://doi.org/10.3389/fneur.2018.01063
37 BN Flores, X Li, AM Malik et al. An intramolecular salt bridge linking TDP43 RNA binding, protein stability, and TDP43-dependent neurodegeneration. Cell Rep 2019;27:1133–1150. e8.
https://doi.org/10.1016/j.celrep.2019.03.093
38 M Galloux, J Risso-Ballester, C-A Richard et al. Minimal elements required for the formation of respiratory syncytial virus cytoplasmic inclusion bodies In Vivo and In Vitro. mBio 2020;11::e01202-20.
https://doi.org/10.1128/mBio.01202-20
39 Y Gao, G Pei, D Li et al. Multivalent m(6)A motifs promote phase separation of YTHDF proteins. Cell Res 2019;29:767–9.
https://doi.org/10.1038/S41422-019-0210-3
40 M Gerstung, C Jolly, I Leshchiner et al. The evolutionary history of 2,658 cancers. Nature 2020;578:122–8.
41 AD Gitler, P Dhillon, J Shorter. Neurodegenerative disease: models, mechanisms, and a new hope. Dis Model Mech 2017;10:499–502.
https://doi.org/10.1242/dmm.030205
42 B Gollan, G Grabe, C Michaux et al. Bacterial persisters and infection: past, present, and progressing. Annu Rev Microbiol 2019;73:359–85.
https://doi.org/10.1146/annurev-micro-020518-115650
43 ZR Grese, AC Bastos, LD Mamede et al. Specific RNA interactions promote TDP-43 multivalent phase separation and maintain liquid properties. EMBO Rep 2021;22:e53632.
https://doi.org/10.15252/embr.202153632
44 C Guo, Z Che, J Yue et al. ENL initiates multivalent phase separation of the super elongation complex (SEC) in controlling rapid transcriptional activation. Sci Adv 2020;6:eaay4858.
https://doi.org/10.1126/sciadv.aay4858
45 Guseva, Serafima, Milles, Sigrid, Jensen, Malene Ringkjøing, et al Measles virus nucleo-and phosphoproteins form liquid-like phase-separated compartments that promote nucleocapsid assembly. Science Advances 2020;6(14):eaaz7095:
https://doi.org/10.1126/sciadv.aaz7095
46 M Hallegger, AM Chakrabarti, FCY Lee et al. TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. Cell 2021;184:4680–4696. e22.
https://doi.org/10.1016/j.cell.2021.07.018
47 J Han, P Chadha, JL Starkey et al. Function of glycoprotein E of herpes simplex virus requires coordinated assembly of three tegument proteins on its cytoplasmic tail. Proc Natl Acad Sci USA 2012;109:19798–803.
https://doi.org/10.1073/pnas.1212900109
48 D Hanahan, RA Weinberg. Hallmarks of cancer: the next generation. Cell 2011;144:646–74.
https://doi.org/10.1016/j.cell.2011.02.013
49 BS Heinrich, Z Maliga, DA Stein et al. Phase transitions drive the formation of vesicular stomatitis virus replication compartments. mBio 2018;9:02290–17.
https://doi.org/10.1128/mBio.02290-17
50 M Hofweber, S Hutten, B Bourgeois et al. Phase separation of FUS is suppressed by its nuclear import receptor and arginine methylation. Cell 2018;173:706–719. e13.
https://doi.org/10.1016/j.cell.2018.03.004
51 S Hu, EC Claud, MW Musch et al. Stress granule formation mediates the inhibition of colonic Hsp70 translation by interferon-γand tumor necrosis factor-α. Am J Physiol Gastrointest Liver Physiol 2010;298:G481–92.
https://doi.org/10.1152/ajpgi.00234.2009
52 G Hu, Z Wu, K Wang et al. Untapped potential of disordered proteins in current druggable human proteome. Curr Drug Targets 2016;17:1198–205.
https://doi.org/10.2174/1389450116666150722141119
53 AA Hyman, CA Weber, F Julicher. Liquid-liquid phase separation in biology. Annu Rev Cell Dev Biol 2014;30:39–58.
https://doi.org/10.1146/annurev-cellbio-100913-013325
54 C Iserman, CA Roden, MA Boerneke et al. Genomic RNA elements drive phase separation of the SARS-CoV-2 nucleocapsid. Mol Cell 2020;80:1078–1091. e6.
https://doi.org/10.1016/j.molcel.2020.11.041
55 Y Itoh, S Iida, S Tamura et al. 1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells. Life Sci Alliance 2021;4:e202001005.
https://doi.org/10.26508/lsa.202001005
56 J Jankovic. Parkinson’s disease: clinical features and diagnosis. J Neurol Neurosurg Psychiatry 2008;79:368–76.
https://doi.org/10.1136/jnnp.2007.131045
57 M Jimenez-Sanchez, F Licitra, BR Underwood et al. Huntington’s disease: mechanisms of pathogenesis and therapeutic strategies. Cold Spring Harb Perspect Med 2017;7:a024240.
https://doi.org/10.1101/cshperspect.a024240
58 J Kang, L Lim, J Song. ATP enhances at low concentrations but dissolves at high concentrations liquid-liquid phase separation (LLPS) of ALS/FTD-causing FUS. Biochem Biophys Res Commun 2018;504:545–51.
https://doi.org/10.1016/j.bbrc.2018.09.014
59 HJ Kim, NC Kim, YD Wang et al. Mutations in prion-like domains in hnRNPa2B1 and hnRNPa1 cause multisystem proteinopathy and ALS. Nature 2013;495:467–73.
60 MY Kim, I Na, JS Kim et al. Rational discovery of antimetastatic agents targeting the intrinsically disordered region of MBD2. Sci Adv 2019a;5:eaav9810.
https://doi.org/10.1126/sciadv.aav9810
61 SS-Y Kim, L Sze, K-P Lam. The stress granule protein G3BP1 binds viral dsRNA and RIG-I to enhance interferon-βresponse. J Biol Chem 2019b;294:6430–8.
https://doi.org/10.1074/jbc.Ra118.005868
62 TH Kim, B Tsang, RM Vernon et al. Phospho-dependent phase separation of FMRP and CAPRIN1 recapitulates regulation of translation and deadenylation. Science 2019c;365:825–9.
https://doi.org/10.1126/science.aax4240
63 S Klein, M Cortese, SL Winter et al. SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography. Nat Commun 2020;11:5885.
https://doi.org/10.1038/S41467-020-19619-7
64 BG Klupp, S Bötcher, H Granzow et al. Complex formation between the UL16 and UL21 tegument proteins of pseudorabies virus. J Virol 2005;79:1510–22.
https://doi.org/10.1128/JVI.79.3.1510-1522.2005
65 KS Kosik, S Han. Tau condensates. Adv Exp Med Biol 2019;1184:327–39.
https://doi.org/10.1007/978-981-32-9358-8_24
66 H Kovar. Dr Jekyll and Mr Hyde: the two faces of the FUS/EWS/TAF15 protein family. Sarcoma 2011;2011:837474.
https://doi.org/10.1155/2011/837474
67 N Le May, S Dubaele, LP De Santis et al. TFIIH transcription factor, a target for the rift valley hemorrhagic fever virus. Cell 2004;116:541–50.
https://doi.org/10.1016/S0092-8674(04)00132-1
68 V Le Sage, A Cinti, S McCarthy et al. Ebola virus VP35 blocks stress granule assembly. Virology 2017;502:73–83.
https://doi.org/10.1016/j.virol.2016.12.012
69 BR Levone, SC Lenzken, M Antonaci et al. FUS-dependent liquid-liquid phase separation is important for DNA repair initiation. J Cell Biol 2021;220:e202008030.
https://doi.org/10.1083/jcb.202008030
70 P Li, S Banjade, H-C Cheng et al. Phase transitions in the assembly of multivalent signalling proteins. Nature 2012;483:336–40.
https://doi.org/10.1038/nature10879
71 Y Li, Y Zhang, X Li et al. Gain-of-function mutations: an emerging advantage for cancer biology. Trends Biochem Sci 2019;44:659–74.
https://doi.org/10.1016/j.tibs.2019.03.009
72 Y Li, ND Roberts, JA Wala et al; PCAWG Structural Variation Working Group. Patterns of somatic structural variation in human cancer genomes. Nature 2020;578:112–21.
73 R Li, T Li, G Lu et al. Programming cell-surface signaling by phase-separation-controlled compartmentalization. Nat Chem Biol 2022;18:1351–60.
https://doi.org/10.1038/S41589-022-01192-3
74 Y Liu, H-B Li, RA Flavell. cGAS activation in phased droplets. Cell Res 2018;28:967–8.
https://doi.org/10.1038/S41422-018-0087-6
75 SY Liu, Y Feng, JJ Wu et al. m(6) A facilitates YTHDF-independent phase separation. J Cell Mol Med 2020;24:2070–2.
https://doi.org/10.1111/jcmm.14847
76 S Lotankar, KS Prabhavalkar, LK Bhatt. Biomarkers for Parkinson’s disease: recent advancement. Neurosci Bull 2017;33:585–97.
https://doi.org/10.1007/S12264-017-0183-5
77 V Lounnas, T Ritschel, J Kelder et al. Current progress in structure-based rational drug design marks a new mindset in drug discovery. Comput Struct Biotechnol J 2013;5:e201302011.
https://doi.org/10.5936/csbj.201302011
78 S Lu, Q Ye, D Singh et al. The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein. Nat Commun 2021;12:502.
https://doi.org/10.1038/S41467-020-20768-y
79 J Lugo-Martinez, V Pejaver, KA Pagel et al. The loss and gain of functional amino acid residues is a common mechanism causing human inherited disease. PLoS Comput Biol 2016;12:e1005091.
https://doi.org/10.1371/journal.pcbi.1005091
80 L Luo, Z Li, T Zhao et al. SARS-CoV-2 nucleocapsid protein phase separates with G3BPs to disassemble stress granules and facilitate viral production. Sci Bull (Beijing) 2021;66:1194–1204.
https://doi.org/10.1016/j.scib.2021.01.013
81 AS Lyon, WB Peeples, MK Rosen. A framework for understanding the functions of biomolecular condensates across scales. Nat Rev Mol Cell Biol 2021;22:215–35.
https://doi.org/10.1038/S41580-020-00303-z
82 IR Mackenzie, AM Nicholson, M Sarkar et al. TIa1 mutations in amyotrophic lateral sclerosis and frontotemporal dementia promote phase separation and alter stress granule dynamics. Neuron 2017;95:808–816. e9.
https://doi.org/10.1016/j.neuron.2017.07.025
83 S Maharana, J Wang, DK Papadopoulos et al. RNA buffers the phase separation behavior of prion-like RNA binding proteins. Science 2018;360:918–21.
https://doi.org/10.1126/science.aar7366
84 LN Makley, JE Gestwicki. Expanding the number of ‘druggable’ targets: non-enzymes and protein-protein interactions. Chem Biol Drug Des 2013;81:22–32.
https://doi.org/10.1111/cbdd.12066
85 P Manivannan, MA Siddiqui, K Malathi. RNase L amplifies interferon signaling by inducing protein kinase R-mediated antiviral stress granules. J Virol 2020;94:e00205-20.
https://doi.org/10.1128/JVI.00205-20
86 JR Mann, AM Gleixner, JC Mauna et al. RNA binding antagonizes neurotoxic phase transitions of TDP-43. Neuron 2019;102:321–338. e8.
https://doi.org/10.1016/j.neuron.2019.01.048
87 SJ Metallo. Intrinsically disordered proteins are potential drug targets. Curr Opin Chem Biol 2010;14:481–8.
https://doi.org/10.1016/j.cbpa.2010.06.169
88 CM Metrick, AL Koenigsberg, EE Heldwein. Conserved outer tegument component UL11 from herpes simplex virus 1 is an intrinsically disordered, RNA-binding protein. mbio 2020;11:e00810-20.
https://doi.org/10.1128/mBio.00810-20
89 A Molliex, J Temirov, J Lee et al. Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization. Cell 2015;163:123–33.
https://doi.org/10.1016/j.cell.2015.09.015
90 Z Monahan, VH Ryan, AM Janke et al. Phosphorylation of the FUS low-complexity domain disrupts phase separation, aggregation, and toxicity. EMBO J 2017;36:2951–67.
https://doi.org/10.15252/embj.201696394
91 A Monette, M Niu, L Chen et al. Pan-retroviral nucleocapsidmediated phase separation regulates genomic RNA positioning and trafficking. Cell Rep 2020;31:107520.
https://doi.org/10.1016/j.celrep.2020.03.084
92 MC Munder, D Midtvedt, T Franzmann et al. A pH-driven transition of the cytoplasm from a fluid-to a solid-like state promotes entry into dormancy. elife 2016;5:e09347.
https://doi.org/10.7554/eLife.09347
93 J Nikolic, R Le Bars, Z Lama et al. Negri bodies are viral factories with properties of liquid organelles. Nat Commun 2017;8:58.
https://doi.org/10.1038/S41467-017-00102-9
94 KM Okonski, CE Samuel. Stress granule formation induced by measles virus is protein kinase PKR dependent and impaired by RNA adenosine deaminase ADAr1. J Virol 2013;87:756–66.
https://doi.org/10.1128/JVI.02270-12
95 K Onomoto, M Jogi, J-S Yoo et al. Critical role of an antiviral stress granule containing RIG-I and PKR in viral detection and innate immunity. PLoS One 2012;7:e43031.
https://doi.org/10.1371/journal.pone.0043031
96 K Onomoto, M Yoneyama, G Fung et al. Antiviral innate immunity and stress granule responses. Trends Immunol 2014;35:420–8.
https://doi.org/10.1016/j.it.2014.07.006
97 M Paget, C Cadena, S Ahmad et al. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA. Mol Cell 2023;83:1180–1196. e8.
https://doi.org/10.1016/j.molcel.2023.03.010
98 BR Parry, IV Surovtsev, MT Cabeen et al. The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity. Cell 2014;156:183–94.
https://doi.org/10.1016/j.cell.2013.11.028
99 A Patel, HO Lee, L Jawerth et al. A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation. Cell 2015;162:1066–77.
https://doi.org/10.1016/j.cell.2015.07.047
100 C Peng, JQ Trojanowski, VM Lee. Protein transmission in neurodegenerative disease. Nat Rev Neurol 2020a;16:199–212.
https://doi.org/10.1038/S41582-020-0333-7
101 Q Peng, L Wang, Z Qin et al. Phase separation of Epstein-Barr virus EBNa2 and its coactivator EBNALP controls gene expression. J Virol 2020b;94:e01771–19.
https://doi.org/10.1128/JVI.01771-19
102 CL Pham, N Shanmugam, M Strange et al. Viral M45 and necroptosis-associated proteins form heteromeric amyloid assemblies. EMBO Rep 2019;20:e46518.
https://doi.org/10.15252/embr.201846518
103 N Poblete-Durán, Y Prades-Pérez, J Vera-Otarola et al. Who regulates whom? An overview of RNA granules and viral infections. Viruses 2016;8:180.
https://doi.org/10.3390/v8070180
104 AE Posey, KM Ruff, TS Harmon et al. Profilin reduces aggregation and phase separation of huntingtin N-terminal fragments by preferentially binding to soluble monomers and oligomers. J Biol Chem 2018;293:3734–46.
https://doi.org/10.1074/jbc.Ra117.000357
105 DS Protter, R Parker. Principles and properties of stress granules. Trends Cell Biol 2016;26:668–79.
https://doi.org/10.1016/j.tcb.2016.05.004
106 C Rabouille, S Alberti. Cell adaptation upon stress: the emerging role of membrane-less compartments. Curr Opin Cell Biol 2017;47:34–42.
https://doi.org/10.1016/j.ceb.2017.02.006
107 M Rask-Andersen, S Masuram, HB Schiöh. The druggable genome: evaluation of drug targets in clinical trials suggests major shifts in molecular class and indication. Annu Rev Pharmacol Toxicol 2014;54:9–26.
https://doi.org/10.1146/annurev-pharmtox-011613-135943
108 S Ray, N Singh, R Kumar et al. alpha-Synuclein aggregation nucleates through liquid-liquid phase separation. Nat Chem 2020;12:705–16.
https://doi.org/10.1038/S41557-020-0465-9
109 WG Rice, JG Supko, L Malspeis et al. Inhibitors of HIV nucleocapsid protein zinc fingers as candidates for the treatment of AIDS. Science 1995;270:1194–7.
https://doi.org/10.1126/science.270.5239.1194
110 RJ Ries, S Zaccara, P Klein et al. m(6)A enhances the phase separation potential of mRNA. Nature 2019;571:424–8.
https://doi.org/10.1038/S41586-019-1374-1
111 J Risso-Ballester,, M Galloux,, J Cao, et al. A condensate-hardening drug blocks RSV replication in vivo. Nature 2021;595(7868):596-599.
https://doi.org/10.1038/S41586-021-03703-z
112 I Ritsch, E Lehmann, L Emmanouilidis et al. Phase separation of heterogeneous nuclear ribonucleoprotein a1 upon specific RNA-binding observed by magnetic resonance. Angew Chem Int Ed Engl 2022;61:e202204311.
https://doi.org/10.1002/anie.202204311
113 B Rodriguez-Martin, EG Alvarez, A Baez-Ortega et al. Pancancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet 2020;52:306–19.
114 P Sanchez-Martin, M Komatsu. p62/SQSTM1—steering the cell through health and disease. J Cell Sci 2018;131:jcS222836.
https://doi.org/10.1242/jcs.222836
115 A Savastano, D Flores, H Kadavath et al. Disease-associated tau phosphorylation hinders tubulin assembly within tau condensates. Angew Chem Int Ed Engl 2021;60:726–30.
https://doi.org/10.1002/anie.202011157
116 R Sengoku. Aging and Alzheimer’s disease pathology. Neuropathology 2020;40:22–9.
https://doi.org/10.1111/neup.12626
117 S Seton-Rogers. SPOP mutations disrupt phase separation. Nat Rev Cancer 2018;18:667.
https://doi.org/10.1038/S41568-018-0066-8
118 G Seydoux, M Zhang, JD Forman-Kay et al. Transitions in the framework of condensate biology. Mol Cell 2023;83:1016–21.
https://doi.org/10.1016/j.molcel.2023.03.014
119 B Shen, Z Chen, C Yu et al. Computational screening of biological phase-separating proteins. Genom Proteom Bioinform 2021;19:13–24.
https://doi.org/10.1016/j.gpb.2020.11.003
120 Y Shin, CP Brangwynne. Liquid phase condensation in cell physiology and disease. Science 2017;357:eaaf4382.
https://doi.org/10.1126/science.aaF4382
121 J Shorter. Prion-like domains program Ewing’s Sarcoma. Cell 2017;171:30–1.
https://doi.org/10.1016/j.cell.2017.09.010
122 M Suarez-Calvet, M Neumann, T Arzberger et al. Monomethylated and unmethylated FUS exhibit increased binding to transportin and distinguish FTLDFUS from ALS-FUS. Acta Neuropathol 2016;131:587–604.
https://doi.org/10.1007/S00401-016-1544-2
123 D Sun, R Wu, J Zheng et al. Polyubiquitin chain-induced p62 phase separation drives autophagic cargo segregation. Cell Res 2018;28:405–15.
https://doi.org/10.1038/S41422-018-0017-7
124 AY Tan, JL Manley. The TET family of proteins: functions and roles in disease. J Mol Cell Biol 2009;1:82–92.
https://doi.org/10.1093/jmcb/mjp025
125 K Taniue, N Akimitsu. Aberrant phase separation and cancer. FEBS J 2021;289:17–39.
https://doi.org/10.1111/febs.15765
126 S Tripathi, HK Shirnekhi, SD Gorman et al. Defining the condensate landscape of fusion oncoproteins. Nat Commun 2023;14:6008.
127 VN Uversky. Intrinsically disordered proteins and novel strategies for drug discovery. Expert Opin Drug Discov 2012;7:475–88.
https://doi.org/10.1517/17460441.2012.686489
128 S Vajda, D Beglov, AE Wakefield et al. Cryptic binding sites on proteins: definition, detection, and druggability. Curr Opin Chem Biol 2018;44:1–8.
https://doi.org/10.1016/j.cbpa.2018.05.003
129 A Voigt, D Herholz, FC Fiesel et al. TDP-43-mediated neuron loss in vivo requires RNA-binding activity. PLoS One 2010;5:e12247.
https://doi.org/10.1371/journal.pone.0012247
130 L Wan, S Chong, F Xuan et al. Impaired cell fate through gain-of-function mutations in a chromatin reader. Nature 2020;577:121–6.
https://doi.org/10.1038/S41586-019-1842-7
131 A Wang, AE Conicella, HB Schmidt et al. A single N-terminal phosphomimic disrupts TDP-43 polymerization, phase separation, and RNA splicing. EMBO J 2018a;37:e97452.
https://doi.org/10.15252/embj.201797452
132 J Wang, JM Choi, AS Holehouse et al. A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins. Cell 2018b;174:688–699. e16.
https://doi.org/10.1016/j.cell.2018.06.006
133 J Wang, L Wang, J Diao et al. Binding to m(6)A RNA promotes YTHDF2-mediated phase separation. Protein Cell 2020;11:304–7.
https://doi.org/10.1007/S13238-019-00660-2
134 Y Wang, C Yu, G Pei et al. Dissolution of oncofusion transcription factor condensates for cancer therapy. Nat Chem Biol 2023;19:1223–1234.
https://doi.org/10.1038/S41589-023-01376-5
135 S Wegmann, B Eftekharzadeh, K Tepper et al. Tau protein liquid-liquid phase separation can initiate tau aggregation. EMBO J 2018;37:e98049.
https://doi.org/10.15252/embj.201798049
136 JH Weishaupt, T Hyman, I Dikic. Common molecular pathways in amyotrophic lateral sclerosis and frontotemporal dementia. Trends Mol Med 2016;22:769–83.
https://doi.org/10.1016/j.molmed.2016.07.005
137 RJ Wheeler. Therapeutics—how to treat phase separationassociated diseases. Emerg Top Life Sci 2020;4:331–42.
https://doi.org/10.1042/ETLS20190176
138 RJ Wheeler, AA Hyman. Controlling compartmentalization by non-membrane-bound organelles. Philos Trans R Soc London Ser B 2018;373:20170193.
https://doi.org/10.1098/rstb.2017.0193
139 JR Wheeler, T Matheny, S Jain et al. Distinct stages in stress granule assembly and disassembly. Elife 2016;5:e18413.
https://doi.org/10.7554/eLife.18413
140 RJ Wheeler, HO Lee, I Poser et al. Small molecules for modulating protein driven liquid-liquid phase separation in treating neurodegenerative disease. ???BioRxiv 2019.
https://doi.org/10.1101/721001
141 T Wyss-Coray. Ageing, neurodegeneration and brain rejuvenation. Nature 2016;539:180–6.
https://doi.org/10.1038/nature20411
142 W Xu, G Pei, H Liu et al. Compartmentalization-aided interaction screening reveals extensive high-order complexes within the SARS-CoV-2 proteome. Cell Rep 2021;36:109482.
https://doi.org/10.1016/j.celrep.2021.109482
143 J Yang, X Yang. Phase transition of Huntingtin: factors and pathological relevance. Front Genet 2020;11:754.
https://doi.org/10.3389/fgene.2020.00754
144 S Yasuda, H Tsuchiya, A Kaiho et al. Stress-and ubiquitylation-dependent phase separation of the proteasome. Nature 2020;578:296–300.
https://doi.org/10.1038/S41586-020-1982-9
145 P.-C. Yeh, (2009). Interactions between the tegument proteins, UL11 and UL16, and the glycoprotein E of Herpes Simplex Virus.
146 A Zbinden, M Perez-Berlanga, P De Rossi et al. Phase separation and neurodegenerative diseases: a disturbance in the force. Dev Cell 2020;55:45–68.
https://doi.org/10.1016/j.devcel.2020.09.014
147 D Zhao, W Xu, X Zhang et al. Understanding the phase separation characteristics of nucleocapsid protein provides a new therapeutic opportunity against SARS-CoV-2. Protein Cell 2021;12:734–40.
https://doi.org/10.1007/S13238-021-00832-z
148 Y Zhou, JM Su, CE Samuel et al. Measles virus forms inclusion bodies with properties of liquid organelles. J Virol 2019;93:e00948-19.
https://doi.org/10.1128/JVI.00948-19
149 G Zhu, J Xie, W Kong et al. Phase separation of disease-associated SHP2 mutants underlies MAPK hyperactivation. Cell 2020;183:490–502.e18.
https://doi.org/10.1016/j.cell.2020.09.002
150 G Zhu, J Xie, Z Fu et al. Pharmacological inhibition of SRC-1 phase separation suppresses YAP oncogenic transcription activity. Cell Res 2021;31:1028–31.
https://doi.org/10.1038/S41422-021-00504-x
[1] PAC-0493-23149-SYZ_suppl_1 Download
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed